MCP Documentation Server

mcp-documentation-server

Skill by ara.so — MCP Skills collection.

MCP Documentation Server provides local-first document management with semantic search capabilities. It uses an embedded Orama vector database for hybrid full-text and vector search, intelligent parent-child chunking for better context, and optional Google Gemini AI integration for advanced document analysis.

Installation

Quick Start with MCP Client

Add to your MCP client configuration (e.g., Claude Desktop ~/Library/Application Support/Claude/claude_desktop_config.json):

{
  "mcpServers": {
    "documentation": {
      "command": "npx",
      "args": ["-y", "@andrea9293/mcp-documentation-server"]
    }
  }
}

With Environment Variables

{
  "mcpServers": {
    "documentation": {
      "command": "npx",
      "args": ["-y", "@andrea9293/mcp-documentation-server"],
      "env": {
        "MCP_BASE_DIR": "/path/to/workspace",
        "GEMINI_API_KEY": "your-gemini-api-key",
        "MCP_EMBEDDING_MODEL": "Xenova/paraphrase-multilingual-mpnet-base-v2",
        "START_WEB_UI": "true",
        "WEB_PORT": "3080"
      }
    }
  }
}

Development Installation

git clone https://github.com/andrea9293/mcp-documentation-server.git
cd mcp-documentation-server
npm install
npm run build

Configuration

Environment Variables

Embedding Models

Fast (default):

• Xenova/all-MiniLM-L6-v2 — 384 dimensions, ~80MB

High Quality (recommended):

• Xenova/paraphrase-multilingual-mpnet-base-v2 — 768 dimensions, ~420MB, multilingual

⚠️ Changing models requires re-indexing all documents (embeddings are incompatible).

Storage Structure

~/.mcp-documentation-server/
├── data/
│   ├── orama-chunks.msp      # Vector DB (child chunks + embeddings)
│   ├── orama-docs.msp        # Document DB (full content + metadata)
│   ├── orama-parents.msp     # Parent chunks DB (context sections)
│   ├── migration-complete.flag
│   └── *.md                  # Markdown document copies
└── uploads/                  # Drop files here for processing

MCP Tools

Document Management

add_document

Add a new document to the knowledge base.

// Tool call
{
  "title": "API Reference",
  "content": "# Authentication\nUse Bearer tokens...",
  "metadata": {
    "category": "api",
    "version": "2.0",
    "author": "team"
  }
}

Response includes document ID, chunk count, and timing stats.

list_documents

List all documents with metadata and previews.

// Tool call (no parameters required)

// Returns array of documents:
[
  {
    "id": "doc_abc123",
    "title": "API Reference",
    "preview": "# Authentication\nUse Bearer...",
    "metadata": { "category": "api" },
    "created": "2025-01-15T10:30:00Z",
    "updated": "2025-01-15T10:30:00Z"
  }
]

get_document

Retrieve full document content by ID.

// Tool call
{
  "id": "doc_abc123"
}

// Returns complete document with metadata and full content

delete_document

Remove a document and all associated data.

// Tool call
{
  "id": "doc_abc123"
}

// Deletes document, chunks, embeddings, and backup files

File Processing

process_uploads

Process all files from the uploads folder.

// Tool call (no parameters)
// Processes .txt, .md, .pdf files from ~/.mcp-documentation-server/uploads/

// Returns:
{
  "processed": 3,
  "failed": 0,
  "results": [
    {
      "filename": "guide.md",
      "success": true,
      "documentId": "doc_xyz789",
      "chunks": 12
    }
  ]
}

get_uploads_path

Get the absolute path to the uploads folder.

// Tool call (no parameters)
// Returns: "/Users/username/.mcp-documentation-server/uploads"

list_uploads_files

List files in the uploads folder.

// Tool call (no parameters)

// Returns:
[
  {
    "name": "api-guide.md",
    "size": 45678,
    "sizeFormatted": "44.6 KB",
    "extension": ".md"
  }
]

get_ui_url

Get the Web UI URL.

// Tool call (no parameters)
// Returns: "http://localhost:3080"

Search Tools

search_documents

Semantic vector search within a specific document.

// Tool call
{
  "documentId": "doc_abc123",
  "query": "authentication methods",
  "limit": 5
}

// Returns:
{
  "results": [
    {
      "content": "Bearer token authentication is used...",
      "parentContent": "# Authentication\nBearer token authentication...",
      "score": 0.92,
      "documentId": "doc_abc123",
      "documentTitle": "API Reference"
    }
  ],
  "total": 5
}

search_all_documents

Hybrid full-text + vector search across all documents.

// Tool call
{
  "query": "rate limiting configuration",
  "limit": 10
}

// Returns deduplicated results sorted by relevance
// Includes both exact text matches and semantic similarity

get_context_window

Fetch surrounding chunks for richer context.

// Tool call
{
  "documentId": "doc_abc123",
  "chunkIndex": 5,
  "windowSize": 2
}

// Returns chunks [3, 4, 5, 6, 7] with the target chunk at index 5
// Useful for giving LLMs broader context around a search result

search_documents_with_ai

AI-powered search using Google Gemini (requires GEMINI_API_KEY).

// Tool call
{
  "documentIds": ["doc_abc123", "doc_xyz789"],
  "query": "How do I implement rate limiting with Redis?",
  "conversationHistory": [
    {
      "role": "user",
      "content": "What caching options are available?"
    },
    {
      "role": "assistant",
      "content": "Redis and Memcached are supported..."
    }
  ]
}

// Returns AI-generated answer with context and sources

Common Patterns

Setting Up a Knowledge Base

// 1. Add documents programmatically
const apiDoc = await mcp.call("add_document", {
  title: "REST API Guide",
  content: "# REST API\n\n## Endpoints...",
  metadata: { type: "api", version: "1.0" }
});

// 2. Or drop files in uploads folder
const uploadsPath = await mcp.call("get_uploads_path");
// Copy files to uploadsPath, then:
const result = await mcp.call("process_uploads");

// 3. Verify documents
const docs = await mcp.call("list_documents");
console.log(`${docs.length} documents indexed`);

Semantic Search Workflow

// Search across all documents
const results = await mcp.call("search_all_documents", {
  query: "database connection pooling",
  limit: 5
});

// Get more context for top result
if (results.results.length > 0) {
  const topResult = results.results[0];
  const context = await mcp.call("get_context_window", {
    documentId: topResult.documentId,
    chunkIndex: topResult.chunkIndex,
    windowSize: 3
  });
  
  // context.chunks contains surrounding sections
}

AI-Assisted Research

// Use Gemini for complex queries
const answer = await mcp.call("search_documents_with_ai", {
  documentIds: ["doc_1", "doc_2"],
  query: "Compare authentication approaches and recommend best practices",
  conversationHistory: []
});

// answer contains:
// - AI-generated response
// - Source chunks with citations
// - Confidence scores

Batch Document Processing

// Process multiple files efficiently
const files = await mcp.call("list_uploads_files");
console.log(`Found ${files.length} files to process`);

const result = await mcp.call("process_uploads");

result.results.forEach(item => {
  if (item.success) {
    console.log(`✓ ${item.filename}: ${item.chunks} chunks`);
  } else {
    console.error(`✗ ${item.filename}: ${item.error}`);
  }
});

Managing Document Lifecycle

// List and filter documents
const allDocs = await mcp.call("list_documents");
const apiDocs = allDocs.filter(doc => 
  doc.metadata?.category === "api"
);

// Update a document (delete + re-add)
await mcp.call("delete_document", { id: "doc_old" });
await mcp.call("add_document", {
  title: "Updated API Docs",
  content: updatedContent,
  metadata: { category: "api", version: "2.0" }
});

Web UI

Access the built-in web interface at http://localhost:3080 (default).

Features:

• Dashboard with document statistics
• Upload drag & drop interface
• Visual search across all documents
• Document browser with delete/view
• AI search interface (if Gemini key configured)
• Context window explorer

Disable with START_WEB_UI=false or change port with WEB_PORT.

Troubleshooting

Embeddings Not Generated

Symptom: Search returns no results or poor results.

Solution:

# Check if model is downloaded
ls ~/.cache/huggingface/

# Force re-download by clearing cache
rm -rf ~/.cache/huggingface/
# Restart server to re-download

Model Change Not Taking Effect

Symptom: Changed MCP_EMBEDDING_MODEL but search quality unchanged.

Solution:

# Delete existing database
rm ~/.mcp-documentation-server/data/orama-*.msp

# Re-add all documents
# Server will recreate database with new model dimensions

Large File Processing Fails

Symptom: File upload times out or fails.

Solution:

{
  "env": {
    "MCP_STREAMING_ENABLED": "true",
    "MCP_STREAM_FILE_SIZE_LIMIT": "5242880"
  }
}

Reduces threshold to 5MB to trigger streaming mode earlier.

AI Search Not Available

Symptom: search_documents_with_ai tool missing.

Solution:

• Verify GEMINI_API_KEY is set in configuration
• Get API key from https://aistudio.google.com/app/apikey
• Restart MCP server after adding key

Port Already in Use

Symptom: Web UI fails to start with EADDRINUSE.

Solution:

{
  "env": {
    "WEB_PORT": "3081"
  }
}

Or disable Web UI: "START_WEB_UI": "false"

Memory Issues with Large Documents

Symptom: Server crashes with out-of-memory error.

Solution:

• Enable streaming: MCP_STREAMING_ENABLED=true
• Reduce chunk size: Process files individually
• Use more efficient model: Xenova/all-MiniLM-L6-v2 (384 dims)

Migration from Legacy JSON

Symptom: Old documents not appearing.

Solution: The server automatically migrates legacy JSON documents on first startup. Check:

ls ~/.mcp-documentation-server/data/migration-complete.flag

If flag exists but documents missing, check logs for migration errors.

Development

Run in development mode:

npm run dev       # MCP server with hot reload
npm run inspect   # FastMCP web UI for testing tools
npm run web       # Web UI only (development)

Build and run production:

npm run build
npm start

Architecture

• FastMCP — MCP server framework with stdio transport
• Orama — Embedded vector database (3 instances: docs, chunks, parents)
• Transformers.js — Local embedding generation (@xenova/transformers)
• Parent-Child Chunking — Large context parents + small precise children
• LRU Cache — In-memory embedding cache for performance
• Streaming Reader — Handle large files without memory bloat

Data flow:

1. Document → IntelligentChunker → Parent chunks + Child chunks
2. Child chunks → EmbeddingProvider → Vectors (384/768 dims)
3. Vectors + chunks → OramaStore → Persisted to disk
4. Query → Hybrid search (text + vector) → Deduplicated by parent → Results with context